This vignette provides the code using Starfysh spot deconvolution on given signatures through integrative spatial deconvolution from multiple samples. The datasets here include 19 distinct TLS postivie ccRCC tumor samples from which 9 are responders to ICI treatment and 10 are non-responders.
#Import needed modules
import os
import numpy as np
import pandas as pd
import torch
import matplotlib.pyplot as plt
import matplotlib.font_manager
from matplotlib import rcParams
import seaborn as sns
sns.set_style('white')
font_list = []
fpaths = matplotlib.font_manager.findSystemFonts()
for i in fpaths:
try:
f = matplotlib.font_manager.get_font(i)
font_list.append(f.family_name)
except RuntimeError:
pass
font_list = set(font_list)
plot_font = 'Helvetica' if 'Helvetica' in font_list else 'FreeSans'
rcParams['font.family'] = plot_font
rcParams.update({'font.size': 10})
rcParams.update({'figure.dpi': 300})
rcParams.update({'figure.figsize': (3,3)})
rcParams.update({'savefig.dpi': 500})
import warnings
warnings.filterwarnings('ignore')
#Load starfysh
from starfysh import (AA, utils, plot_utils, post_analysis)
from starfysh import starfysh as sf_model
Create sample meta info
meta_info = [['P_1','P_1','processed_data/P_1/'],#Already downloaded, #First one is the name of the folder containing the data
['P_2','P_2','processed_data/P_2/'], #
['P_3','P_3','processed_data/P_3/'],#Already downloaded
['P_4','P_4','processed_data/P_4/'],#Already downloaded
['P_5','P_5','processed_data/P_5/'],#Already downloaded
['P_6','P_6','processed_data/P_6/'],#Already downloaded
['P_7','P_7','processed_data/P_7/'],#Already downloaded
['P_8','P_8','processed_data/P_8/'], #Already downloaded
['P_9','P_9','processed_data/P_9/'], #
['P_10','P_10','processed_data/P_10/'],#Already downloaded, #First one is the name of the folder containing the data
['P_11','P_11','processed_data/P_11/'], #
['P_12','P_12','processed_data/P_12/'],#Already downloaded
['P_13','P_13','processed_data/P_13/'],#Already downloaded
['P_14','P_14','processed_data/P_14/'],#Already downloaded
['P_15','P_15','processed_data/P_15/'],#Already downloaded
['P_16','P_16','processed_data/P_16/'],#Already downloaded
['P_17','P_17','processed_data/P_17/'], #Already downloaded
['P_18','P_18','processed_data/P_18/'],
['P_19','P_19','processed_data/P_19/'],
]
#CID44971_TNBC
meta_info = pd.DataFrame(meta_info,columns=['sample','anonymized_id','visiumPath'])
# Specify data paths
data_path = 'processed_data/' # root data directory
output_path = 'Starfysh_results/'
sample_id2 = 'outs' #name of the folder containing the data
#data_path = '../ToyData/'
#output_path = '../ToyData/Results_integrated/'
sig_file_name = 'Starfysh_results/Signatures_Starfysh.csv' #This is the Supplementary Table S13
print(meta_info)
for sample_id in meta_info['sample']:
print(sample_id)
data_path2 = meta_info['visiumPath'][list(meta_info['sample']).index(sample_id)]
print(data_path2)
adata_all = []
adata_normed_all = []
img_metadata_all = {}
for sample_id in meta_info['sample']:
print(sample_id)
data_path2 = meta_info['visiumPath'][list(meta_info['sample']).index(sample_id)]
adata, adata_normed = utils.load_adata(data_folder=data_path2, # root data directory
sample_id=sample_id2, # sample_id
n_genes=2000 # number of highly variable genes to keep
)
adata_all.append(adata)
adata_normed_all.append(adata_normed)
img_metadata = utils.preprocess_img(data_path2,
sample_id2,
adata_index=adata.obs.index,
hchannel=True #Must be true otherwise POE wont work
)
#From: https://github.com/azizilab/starfysh/issues/31
adata.obs['anonymized_id']=meta_info['anonymized_id'][list(meta_info['sample']).index(sample_id)]
#adata.obs['RECIST_R_nR']=meta_info['RECIST_R_nR'][list(meta_info['sample']).index(sample_id)] #Clinical data can be
#demanded to authors
adata.obs['patient']=meta_info['sample'][list(meta_info['sample']).index(sample_id)]
adata.obs['sample']=meta_info['sample'][list(meta_info['sample']).index(sample_id)]
#sample_id_3 = meta_info['anonymized_id'][list(meta_info['sample']).index(sample_id)]
adata.obs_names = adata.obs_names+'-'+sample_id
adata_normed.obs['anonymized_id']=adata.obs['anonymized_id']
adata_normed.obs['patient']=adata.obs['patient']
#adata_normed.obs['RECIST_R_nR']=adata.obs['RECIST_R_nR'] #Clinical data can be
#demanded to authors
img_metadata['map_info'].index = img_metadata['map_info'].index+'-'+sample_id
img_metadata_all[sample_id] = img_metadata
# Save concat data
import anndata
import scanpy as sc
adata_all = anndata.concat(adata_all)
adata_normed_all = anndata.concat(adata_normed_all)
sc.pp.highly_variable_genes(adata_normed_all)
adata_all.uns = adata_normed_all.uns
adata_all.var = adata_normed_all.var
#Check
print(adata_all)
print(adata_normed_all)
AnnData object with n_obs × n_vars = 75259 × 13200
obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'hvg'
obsm: 'spatial'
AnnData object with n_obs × n_vars = 75259 × 13200
obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'hvg'
obsm: 'spatial'
# Load signatures
gene_sig = pd.read_csv(os.path.join(sig_file_name))
gene_sig = utils.filter_gene_sig(gene_sig, adata_all.to_df())
gene_sig.head()
| Tcm | Tem | Tfh | Treg | Activated CD8 | Dysfunc CD8 | Terminal exhaustion | Precursor exhaustion | NK | B cells memory | ... | Monocytes | cDC | pDC | CAFs MSC iCAF-like | CAFs myCAF-like | Endothelial | PT_like | ProInflammatory | EMT_like | PI3K | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | CCR7 | IL7R | CXCL13 | TNFRSF4 | CD69 | NPEPPS | CD3G | TCF7 | GNLY | MS4A1 | ... | LYZ | CD80 | IL3RA | APOD | COL1A1 | ACKR1 | TRPM3 | AL078604.4 | EEF1G | ERBB4 |
| 1 | LTB | ANXA1 | NMB | LTB | CCR7 | NOTCH2 | FASLG | MS4A4A | XCL1 | CD79A | ... | IL1B | CD86 | LILRA4 | DCN | COL1A2 | FABP4 | PBX1 | BIRC3 | FAU | GRHL2 |
| 2 | IL7R | CXCR4 | NR3C1 | IL32 | CD27 | CABLES1 | ID2 | TNFSF8 | XCL2 | CD83 | ... | G0S2 | CCR7 | CD123 | PTGDS | COL3A1 | PLVAP | SLC6A13 | DCLK1 | UBA52 | SIM2 |
| 3 | SARAF | KLRB1 | DUSP4 | BATF | BTLA | CERK | LAG3 | CXCL10 | AREG | CD37 | ... | TYROBP | CD1A | TCF4 | CFD | LUM | RAMP2 | SLC17A4 | PDE10A | MIF | SCHLAP1 |
| 4 | SELL | TNFAIP3 | TNFRSF18 | FOXP3 | CD40LG | MTMR3 | RGS1 | EEF1B2 | KLRD1 | BANK1 | ... | FCN1 | CD1C | IRF7 | LUM | SFRP2 | VWF | SLC6A12 | FKBP5 | EEF2 | ESRP1 |
5 rows × 25 columns
#Save data
# Save concat data
import anndata
import scanpy as sc
#adata_all.write(os.path.join(output_path, 'adata_all.h5ad'))
#adata_normed_all.write(os.path.join(output_path, 'adata_normed_all.h5ad'))
... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical ... storing 'patient' as categorical ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical ... storing 'patient' as categorical
#Load if needed
# Save concat data
import anndata
import scanpy as sc
adata_all = sc.read_h5ad(os.path.join(output_path, 'adata_all.h5ad'))
adata_normed_all = sc.read_h5ad(os.path.join(output_path, 'adata_normed_all.h5ad'))
from starfysh.AA import ArchetypalAnalysis
def assign_archetypes(anchor_df, r=30):
"""
Assign best 1-1 mapping of archetype community to its closest anchor community (cell-type specific anchor spots)
Criteria: choose the top cell type in which its anchors belongs to the top r neighbors to the given archetype
Parameters
----------
anchor_df : pd.DataFrame
Dataframe of anchor spot indices
` r : int
Resolution parameter to threshold archetype - anchor mapping
Returns
-------
map_df : pd.DataFrame
DataFrame of overlapping spot ratio of each anchor `i` to archetype `j`
map_dict : dict
Dictionary of cell type -> mapped archetype
"""
assert aa_model.arche_df is not None, "Please compute archetypes & assign nearest-neighbors first!"
n_nbrs, n_archetypes = aa_model.arche_df.shape # number of archetypal spots for each archtype, number of archetypes
x_concat = np.vstack([aa_model.count, aa_model.archetype])
anchor_nbrs = anchor_df.values
archetypal_nbrs = aa_model._get_knns(x_concat, n_nbrs=r, indices=aa_model.n_spots+aa_model.major_idx).T # r-nearest nbrs to each archetype
print(archetypal_nbrs.shape)
overlaps = np.array(
[
[
len(np.intersect1d(anchor_nbrs[:, i], archetypal_nbrs[:, j]))
for j in range(archetypal_nbrs.shape[1])
]
for i in range(anchor_nbrs.shape[1])
]
)
overlaps_df = pd.DataFrame(overlaps, index=anchor_df.columns, columns=aa_model.arche_df.columns)
arche_argmaxs = overlaps.argmax(0)
distance_df = pd.DataFrame(np.zeros([anchor_df.shape[1],
aa_model.arche_df.shape[1]]),
index=anchor_df.columns,
columns=aa_model.arche_df.columns
)
for i in range(distance_df.shape[0]):
for j in range(distance_df.shape[1]):
dist_tmp = 0
for kk in anchor_df.iloc[:,i]:
dist_tmp += np.linalg.norm(aa_model.count[kk,:] -
aa_model.archetype[j,:]
)
distance_df.iloc[i,j] = dist_tmp
map_dict = {}
for k in range(overlaps.shape[0]):
list_ = np.argsort(overlaps[k])[::-1]
for i in list_:
if (np.argsort(overlaps[:,i])[::-1][0]==k):
if ((overlaps[k,:]==overlaps[k,i]).sum()==1):
map_dict[anchor_df.columns[k]]=aa_model.arche_df.columns[i]
break
map_dict2 = {}
for k in range(distance_df.shape[0]):
list_ = np.argsort(np.array(distance_df)[k])
#print(list_)
for i in list_:
if (np.argsort(np.array(distance_df)[:,i])[0]==k):
if ((np.array(distance_df)[k,:]==np.array(distance_df)[k,i]).sum()==1):
map_dict2[anchor_df.columns[k]]=aa_model.arche_df.columns[i]
break
return overlaps_df, distance_df,map_dict,map_dict2
import importlib
importlib.reload(utils)
gene_sig_all = []
visium_args_all = {}
for sample_id in meta_info['anonymized_id']:
print(sample_id)
adata = adata_all[adata_all.obs['anonymized_id']==sample_id]
adata_normed = adata_normed_all[adata_normed_all.obs['anonymized_id']==sample_id]
sc.pp.highly_variable_genes(adata_normed)
adata.uns = adata_normed.uns
adata.var = adata_normed.var
img_metadata = img_metadata_all[sample_id]
visium_args = utils.VisiumArguments(adata,
adata_normed,
gene_sig,
img_metadata,
window_size=4,
sample_id=sample_id2,#'outs'
n_img_chan = 1,
)
adata, adata_normed = visium_args.get_adata()
anchors_df = visium_args.get_anchors()
aa_model = AA.ArchetypalAnalysis(adata_orig=adata,
# n_neighbors=100 #Atgument not detected
)
archetype, arche_dict, major_idx, evs = aa_model.compute_archetypes(cn=100,
#r=5, not used
converge=1e-3,
display=False)
arche_df = aa_model.find_archetypal_spots()
markers_df = aa_model.find_markers(n_markers=30, display=False)
percent_anchor = 0.01
map_df, distance_df,map_dict,map_dict2 = assign_archetypes(anchors_df[:int(percent_anchor*adata.shape[0])],
r=int(percent_anchor*adata.shape[0])
) # here we subset the `r` top archetypes
gene_sig_arch = gene_sig.copy()
for cell_type in map_dict.keys():
arch = map_dict[cell_type]
gene_sig_arch = utils.append_sigs(gene_sig_arch, cell_type, markers_df[arch], n_genes=10)
gene_sig_all.append(gene_sig_arch)
visium_args_all[sample_id] = visium_args
P_1
[2024-04-29 11:05:47] Subsetting highly variable & signature genes ... [2024-04-29 11:05:55] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:05:55] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:05:57] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:06:00] Computing intrinsic dimension to estimate k...
23 components are retained using conditional_number=100.00
[2024-04-29 11:06:01] Estimating lower bound of # archetype as 8... [2024-04-29 11:07:14] 0.8892 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:07:14] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:07:14] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(13, 14) P_2
[2024-04-29 11:07:19] Subsetting highly variable & signature genes ... [2024-04-29 11:08:06] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:08:09] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:08:14] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:08:47] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 11:08:48] Estimating lower bound of # archetype as 11... [2024-04-29 11:11:13] 0.8618 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:11:13] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:11:13] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(47, 16) P_3
[2024-04-29 11:11:27] Subsetting highly variable & signature genes ... [2024-04-29 11:11:59] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:12:00] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:12:04] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:12:27] Computing intrinsic dimension to estimate k...
27 components are retained using conditional_number=100.00
[2024-04-29 11:12:28] Estimating lower bound of # archetype as 12... [2024-04-29 11:14:35] 0.8875 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:14:35] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:14:35] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(38, 16) P_4
[2024-04-29 11:14:48] Subsetting highly variable & signature genes ... [2024-04-29 11:14:56] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:14:57] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:14:59] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:15:06] Computing intrinsic dimension to estimate k... [2024-04-29 11:15:06] Estimating lower bound of # archetype as 12...
30 components are retained using conditional_number=100.00
[2024-04-29 11:17:58] 0.8667 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:17:58] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:17:58] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(20, 18) P_5
[2024-04-29 11:18:05] Subsetting highly variable & signature genes ... [2024-04-29 11:18:58] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:19:00] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:19:05] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:19:42] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 11:19:43] Estimating lower bound of # archetype as 11... [2024-04-29 11:26:03] 0.8954 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:26:03] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:26:03] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(49, 20) P_6
[2024-04-29 11:26:30] Subsetting highly variable & signature genes ... [2024-04-29 11:26:58] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:27:01] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:27:06] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:27:42] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 11:27:43] Estimating lower bound of # archetype as 12... [2024-04-29 11:42:19] 0.7654 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:42:19] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:42:20] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(49, 20) P_7
[2024-04-29 11:43:06] Subsetting highly variable & signature genes ... [2024-04-29 11:44:37] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:44:38] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:44:41] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:44:52] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 11:44:52] Estimating lower bound of # archetype as 16... [2024-04-29 11:48:29] 0.7851 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:48:29] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:48:29] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(25, 20) P_8
[2024-04-29 11:48:38] Subsetting highly variable & signature genes ... [2024-04-29 11:48:59] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:49:00] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:49:03] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:49:19] Computing intrinsic dimension to estimate k...
29 components are retained using conditional_number=100.00
[2024-04-29 11:49:20] Estimating lower bound of # archetype as 10... [2024-04-29 11:52:33] 0.8909 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:52:33] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:52:33] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(32, 16) P_9
[2024-04-29 11:52:43] Subsetting highly variable & signature genes ... [2024-04-29 11:52:50] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:52:50] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:52:52] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:52:54] Computing intrinsic dimension to estimate k... [2024-04-29 11:52:55] Estimating lower bound of # archetype as 12...
30 components are retained using conditional_number=100.00
[2024-04-29 11:54:00] 0.8711 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 11:54:00] Finding 100 nearest neighbors for each archetype... [2024-04-29 11:54:00] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(10, 13) P_10
[2024-04-29 11:54:04] Subsetting highly variable & signature genes ... [2024-04-29 11:54:33] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 11:54:35] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 11:54:40] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 11:55:14] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 11:55:15] Estimating lower bound of # archetype as 8... [2024-04-29 12:00:41] 0.9363 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:00:41] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:00:41] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(47, 21) P_11
[2024-04-29 12:01:05] Subsetting highly variable & signature genes ... [2024-04-29 12:02:07] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:02:09] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:02:14] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:02:52] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:02:52] Estimating lower bound of # archetype as 11... [2024-04-29 12:09:08] 0.9184 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:09:08] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:09:09] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(49, 27) P_12
[2024-04-29 12:09:39] Subsetting highly variable & signature genes ... [2024-04-29 12:10:08] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:10:10] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:10:15] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:10:48] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:10:49] Estimating lower bound of # archetype as 13... [2024-04-29 12:11:49] 0.8439 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:11:49] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:11:49] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(47, 14) P_13
[2024-04-29 12:11:58] Subsetting highly variable & signature genes ... [2024-04-29 12:12:27] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:12:29] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:12:34] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:13:05] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:13:06] Estimating lower bound of # archetype as 8... [2024-04-29 12:18:12] 0.9134 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:18:12] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:18:13] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(45, 26) P_14
[2024-04-29 12:18:29] Subsetting highly variable & signature genes ... [2024-04-29 12:18:51] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:18:53] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:18:57] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:19:17] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:19:17] Estimating lower bound of # archetype as 7... [2024-04-29 12:23:24] 0.9085 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:23:24] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:23:24] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(35, 23) P_15
[2024-04-29 12:23:44] Subsetting highly variable & signature genes ... [2024-04-29 12:24:28] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:24:30] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:24:35] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:25:12] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:25:13] Estimating lower bound of # archetype as 8... [2024-04-29 12:30:53] 0.8859 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:30:53] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:30:54] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(49, 25) P_16
[2024-04-29 12:31:27] Subsetting highly variable & signature genes ... [2024-04-29 12:31:45] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:31:47] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:31:52] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:32:24] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:32:24] Estimating lower bound of # archetype as 7... [2024-04-29 12:37:15] 0.84 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:37:15] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:37:16] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(46, 25) P_17
[2024-04-29 12:37:35] Subsetting highly variable & signature genes ... [2024-04-29 12:38:03] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:38:05] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:38:10] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:38:47] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:38:48] Estimating lower bound of # archetype as 11... [2024-04-29 12:44:57] 0.9504 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:44:58] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:44:58] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(49, 24) P_18
[2024-04-29 12:45:26] Subsetting highly variable & signature genes ... [2024-04-29 12:45:58] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:46:00] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:46:05] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:46:33] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:46:34] Estimating lower bound of # archetype as 10... [2024-04-29 12:52:06] 0.9056 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:52:06] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:52:06] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(43, 21) P_19
[2024-04-29 12:52:23] Subsetting highly variable & signature genes ... [2024-04-29 12:52:57] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 12:52:59] Retrieving & normalizing signature gene expressions...
WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1'] WARNING: genes are not in var_names and ignored: ['FYB', 'IL21'] WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1'] WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L'] WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B'] WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1'] WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86'] WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5'] WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2'] WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1'] WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19'] WARNING: genes are not in var_names and ignored: ['ARG1'] WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83'] WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A'] WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA'] WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3'] WARNING: genes are not in var_names and ignored: ['CTGF'] WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36'] WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3'] WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG'] WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB'] WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']
[2024-04-29 12:53:05] Identifying anchor spots (highly expression of specific cell-type signatures)... [2024-04-29 12:53:41] Computing intrinsic dimension to estimate k...
30 components are retained using conditional_number=100.00
[2024-04-29 12:53:42] Estimating lower bound of # archetype as 10... [2024-04-29 12:59:37] 0.934 variance explained by raw archetypes. Merging raw archetypes within 100 NNs to get major archetypes [2024-04-29 12:59:37] Finding 100 nearest neighbors for each archetype... [2024-04-29 12:59:38] Finding 30 top marker genes for each archetype... ... storing 'sample' as categorical ... storing 'anonymized_id' as categorical ... storing 'RECIST_R_nR' as categorical
(49, 23)
gene_sig
| Tcm | Tem | Tfh | Treg | Activated CD8 | Dysfunc CD8 | Terminal exhaustion | Precursor exhaustion | NK | B cells memory | ... | Monocytes | cDC | pDC | CAFs MSC iCAF-like | CAFs myCAF-like | Endothelial | PT_like | ProInflammatory | EMT_like | PI3K | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | CCR7 | IL7R | CXCL13 | TNFRSF4 | CD69 | NPEPPS | CD3G | TCF7 | GNLY | MS4A1 | ... | LYZ | CD80 | IL3RA | APOD | COL1A1 | ACKR1 | TRPM3 | AL078604.4 | EEF1G | ERBB4 |
| 1 | LTB | ANXA1 | NMB | LTB | CCR7 | NOTCH2 | FASLG | MS4A4A | XCL1 | CD79A | ... | IL1B | CD86 | LILRA4 | DCN | COL1A2 | FABP4 | PBX1 | BIRC3 | FAU | GRHL2 |
| 2 | IL7R | CXCR4 | NR3C1 | IL32 | CD27 | CABLES1 | ID2 | TNFSF8 | XCL2 | CD83 | ... | G0S2 | CCR7 | CD123 | PTGDS | COL3A1 | PLVAP | SLC6A13 | DCLK1 | UBA52 | SIM2 |
| 3 | SARAF | KLRB1 | DUSP4 | BATF | BTLA | CERK | LAG3 | CXCL10 | AREG | CD37 | ... | TYROBP | CD1A | TCF4 | CFD | LUM | RAMP2 | SLC17A4 | PDE10A | MIF | SCHLAP1 |
| 4 | SELL | TNFAIP3 | TNFRSF18 | FOXP3 | CD40LG | MTMR3 | RGS1 | EEF1B2 | KLRD1 | BANK1 | ... | FCN1 | CD1C | IRF7 | LUM | SFRP2 | VWF | SLC6A12 | FKBP5 | EEF2 | ESRP1 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 95 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | ... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 96 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | ... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 97 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | ... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 98 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | ... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 99 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | ... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
100 rows × 25 columns
This step is for identifying the anchor spots and providing prior for model training.
utils.VisiumArguments is called for each sample (performed already when updating the signature using archetypes, stored as 'visium_args_all'), followed by utils_integrate.VisiumArguments_integrate for integrating all priors.
Starfysh calcualates cell-type proportion scores for each spot per sample given the annotated signatures (per cell type) as the model's prior
Each spot will be ranked (anchors_df) based on the prior, which represents the rough estimation of the given cell-type's enrichment
adata_normed_all
AnnData object with n_obs × n_vars = 75259 × 13200
obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'hvg'
obsm: 'spatial'
from starfysh import utils_integrate
importlib.reload(utils_integrate)
sc.pp.highly_variable_genes(adata_normed_all)
adata_all.uns = adata_normed_all.uns
adata_all.var = adata_normed_all.var
visium_args = utils_integrate.VisiumArguments_integrate(adata_all,
adata_normed_all,
gene_sig, ##Stay with normal signature
img_metadata_all,
visium_args_all,
window_size=3,
sample_id=meta_info['sample']
)
[2024-04-29 19:40:18] Subsetting highly variable & signature genes ... [2024-04-29 19:40:21] Smoothing library size by taking averaging with neighbor spots... [2024-04-29 19:40:58] Retrieving & normalizing signature gene expressions... [2024-04-29 19:40:58] Identifying anchor spots (highly expression of specific cell-type signatures)...
import importlib
importlib.reload(sf_model)
from starfysh import utils_integrate
importlib.reload(utils_integrate)
<module 'starfysh.utils_integrate' from '/home/isaias/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/starfysh/utils_integrate.py'>
(1) Model parameters
n_repeats = 1
epochs = 100
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
import importlib
importlib.reload(utils_integrate)
<module 'starfysh.utils_integrate' from '/home/isaias/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/starfysh/utils_integrate.py'>
adata
AnnData object with n_obs × n_vars = 4936 × 13200
obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'hvg', 'cell_types'
obsm: 'spatial'
(2). Model training
model, loss = utils_integrate.run_starfysh(visium_args,
n_repeats=n_repeats,
epochs=epochs,
poe=True, #Means histology to be used...
device=device)
[2024-04-29 20:00:28] Running Starfysh with 1 restarts, choose the model with best parameters... [2024-04-29 20:00:28] === Restart Starfysh 1 === [2024-04-29 20:00:28] Initializing model parameters... [2024-04-29 20:14:26] Epoch[10/100], train_loss: 7163.9827, train_reconst: 6954.7536, train_u: 13.5052,train_z: 36.2660,train_c: 95.8831,train_n: 63.5748 [2024-04-29 20:28:17] Epoch[20/100], train_loss: 6653.4592, train_reconst: 6451.1382, train_u: 12.1844,train_z: 41.8874,train_c: 83.4769,train_n: 64.7722 [2024-04-29 20:42:08] Epoch[30/100], train_loss: 6666.6284, train_reconst: 6469.7888, train_u: 11.8632,train_z: 41.5447,train_c: 78.2523,train_n: 65.1794 [2024-04-29 20:55:50] Epoch[40/100], train_loss: 6518.8326, train_reconst: 6326.1833, train_u: 11.8387,train_z: 40.8535,train_c: 74.3282,train_n: 65.6289 [2024-04-29 21:09:40] Epoch[50/100], train_loss: 6423.5089, train_reconst: 6233.7970, train_u: 11.9583,train_z: 40.5227,train_c: 71.1362,train_n: 66.0947 [2024-04-29 21:23:35] Epoch[60/100], train_loss: 6381.2035, train_reconst: 6193.9551, train_u: 12.1276,train_z: 40.1263,train_c: 68.3863,train_n: 66.6083 [2024-04-29 21:37:49] Epoch[70/100], train_loss: 6342.5779, train_reconst: 6157.7389, train_u: 12.2960,train_z: 39.6013,train_c: 66.2523,train_n: 66.6894 [2024-04-29 21:52:11] Epoch[80/100], train_loss: 6252.4254, train_reconst: 6069.1305, train_u: 12.4573,train_z: 39.4165,train_c: 64.4898,train_n: 66.9313 [2024-04-29 22:06:36] Epoch[90/100], train_loss: 6224.7530, train_reconst: 6043.2759, train_u: 12.5965,train_z: 38.7373,train_c: 63.0056,train_n: 67.1377 [2024-04-29 22:21:00] Epoch[100/100], train_loss: 6199.6327, train_reconst: 6019.8916, train_u: 12.7062,train_z: 38.0655,train_c: 61.8222,train_n: 67.1472 [2024-04-29 22:21:00] Saving the best-performance model... [2024-04-29 22:21:00] === Finished training ===
# Save model
torch.save(model.state_dict(), os.path.join(output_path, 'integ_model.pt'))
inference_outputs, generative_outputs = sf_model.model_eval_integrate(model,
visium_args.adata,
visium_args,
poe=True,
device=device
)
rv: px_r_poe can't be stored
##Extract integrated object to a different object
adata_integrate = visium_args.adata.copy()
adata_integrate.shape
(75259, 2738)
adata_inte_2 = adata_integrate.copy() #Copy just in case
#save integrated object
adata_inte_2.write(os.path.join(output_path,'adata_integrated.h5ad'))
##
# Deconvolution prediction
prop_pred_df = pd.DataFrame(adata_integrate.obsm['qc_m'], index=adata_integrate.obs_names, columns=gene_sig.columns)
prop_pred_df
##Save deconvolution values
##Export results from deconvolution...
prop_pred_df.to_csv(os.path.join(output_path,'Starfysh_integrated_obs_all.csv'), index=True) ##This file is needed
#to reproduce Figure 3 and 4
###UMAP before sample integration
adata_all2 = adata_all[:, adata_integrate.var_names]
sc.pp.neighbors(adata_all2, use_rep='X', n_neighbors=20)
sc.tl.umap(adata_all2, min_dist=0.2)
#Plot
fig, ax = plt.subplots(1, 1, figsize=(10, 10), dpi=200)
ax = sc.pl.umap(adata_all2, color='anonymized_id',
frameon=False, s=25, ax=ax,
title='UMAP without Starfysh sample integration'
)
fig.savefig(os.path.join(output_path,'UMAP_notIntegrated.pdf'),transparent=True,dpi=1000)
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found. [2024-04-30 09:03:58] findfont: Font family 'FreeSans' not found.
###UMAP after sample integration
###Add deconvolution values stored in 'obsm'['qc_m']
adata_integrate.obs[gene_sig.columns]=pd.DataFrame(adata_integrate.obsm['qc_m'],
columns=gene_sig.columns,
index=adata_integrate.obs_names)
sc.pp.neighbors(adata_integrate,use_rep='qc_m',n_neighbors=20)
sc.tl.umap(adata_integrate, min_dist=0.2)
#Plot
fig, ax = plt.subplots(1, 1, figsize=(10,10), dpi=300)
ax = sc.pl.umap(adata_integrate,color='anonymized_id',
frameon=False, s=5, ax=ax,
title='UMAP after Starfysh sample integration'
)
fig.savefig(os.path.join(output_path,'UMAP_Integrated.pdf'),transparent=True,dpi=1000)
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found. [2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
####UMAP plotting some pops of interest....
#For Treg
sc.settings.set_figure_params(dpi=300, facecolor='white')
sc.settings.set_figure_params(dpi=500, facecolor='white')
fig,ax = plt.subplots(1,1,figsize=(4,3.2),dpi=500)
sc.pl.umap(adata_integrate,color="Treg",frameon=False,
vmax=0.2,
s=10,
cmap='Spectral_r',
ax=ax,
title=''
)
fig.savefig(os.path.join(output_path,'UMAP_Integrated_Treg.pdf'),transparent=True,dpi=1000,bbox_inches='tight')
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found. [2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.